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- PDB-8bcv: Photosystem I assembly intermediate of Avena sativa -

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Basic information

Entry
Database: PDB / ID: 8bcv
TitlePhotosystem I assembly intermediate of Avena sativa
Components
  • (Chlorophyll a-b binding protein ...Light-harvesting complexes of green plants) x 4
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 9
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / PSI structure / assembly intermediate / Monocotyledons / etiolation
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast ...thylakoid membrane / photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site ...Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE ...BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / Antheraxanthin / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesAvena sativa (oats)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsNaschberger, A. / Amunts, A. / Nelson, N.
Funding support Sweden, Israel, 3items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchARC19-0051 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
Israel Science Foundation569/17 Israel
CitationJournal: To Be Published
Title: Photosystem I assembly intermediate of Avena sativa
Authors: Naschberger, A. / Amunts, A. / Nelson, N.
History
DepositionOct 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
H: Photosystem I reaction center subunit VI
I: Photosystem I reaction center subunit VIII
L: Photosystem I reaction center subunit XI
F: Photosystem I reaction center subunit III
G: Photosystem I reaction center subunit V
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit X
1: Chlorophyll a-b binding protein 1, chloroplastic
2: Chlorophyll a-b binding protein 2, chloroplastic
3: Chlorophyll a-b binding protein 3, chloroplastic
4: Chlorophyll a-b binding protein 4, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)586,619240
Polymers408,68616
Non-polymers177,932224
Water12,665703
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PsaA


Mass: 83263.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) / References: UniProt: A0A3G1AUL2, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 82605.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) / References: UniProt: A0A3G1AZK6, photosystem I

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Protein , 1 types, 1 molecules C

#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8909.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) / References: UniProt: A0A3G1ATU7, photosystem I

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Photosystem I reaction center subunit ... , 9 types, 9 molecules DEHILFGJK

#4: Protein Photosystem I reaction center subunit II /


Mass: 22081.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)
#5: Protein Photosystem I reaction center subunit IV /


Mass: 15298.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)
#6: Protein Photosystem I reaction center subunit VI /


Mass: 10088.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)
#7: Protein/peptide Photosystem I reaction center subunit VIII / / PsaI


Mass: 3995.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) / References: UniProt: A0A3G1AZM6
#8: Protein Photosystem I reaction center subunit XI /


Mass: 22575.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)
#9: Protein Photosystem I reaction center subunit III /


Mass: 19346.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)
#10: Protein Photosystem I reaction center subunit V /


Mass: 15113.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)
#11: Protein Photosystem I reaction center subunit IX /


Mass: 5849.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)
#12: Protein Photosystem I reaction center subunit X /


Mass: 13583.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)

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Chlorophyll a-b binding protein ... , 4 types, 4 molecules 1234

#13: Protein Chlorophyll a-b binding protein 1, chloroplastic / Lhca1


Mass: 26137.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) / References: UniProt: A0A482JYH1
#14: Protein Chlorophyll a-b binding protein 2, chloroplastic


Mass: 22706.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)
#15: Protein Chlorophyll a-b binding protein 3, chloroplastic


Mass: 29344.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)
#16: Protein Chlorophyll a-b binding protein 4, chloroplastic


Mass: 27786.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)

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Sugars , 2 types, 21 molecules

#24: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#25: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 13 types, 906 molecules

#17: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 140 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#21: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical ChemComp-C7Z / (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical ChemComp-QDL / Antheraxanthin / (1~{R},3~{S},6~{S})-1,5,5-trimethyl-6-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-7-oxabicyclo[4.1.0]heptan-3-ol


Mass: 584.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O3 / Feature type: SUBJECT OF INVESTIGATION
#31: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Assembly Intermediate of PSI from Avena sativa / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Avena sativa (oats)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2100 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 51.346 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96997 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00938874
ELECTRON MICROSCOPYf_angle_d1.06655177
ELECTRON MICROSCOPYf_dihedral_angle_d10.98613113
ELECTRON MICROSCOPYf_chiral_restr0.0474758
ELECTRON MICROSCOPYf_plane_restr0.00511787

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